PDB-3f6n: Crystal structure of the virion-associated protein P3 from Caulim...

ID or keywords:

Entry

Database: PDB / ID: 3f6n

Title

Crystal structure of the virion-associated protein P3 from Caulimovirus

Components

Virion-associated protein

Keywords

VIRAL PROTEIN / DNA-BINDING PROTEIN / COILED-COIL / TETRAMER / DNA-binding / Virion

Function / homology

Function and homology information

host cell plasmodesma / virion component / DNA binding
Similarity search - Function

Biological species

Cauliflower mosaic virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.1 Å

Authors

Hoh, F. / Uzest, M. / Blanc, S. / Dumas, C.

Citation

Journal: J.Virol. / Year: 2010
Title: Structural insights into the molecular mechanisms of cauliflower mosaic virus transmission by its insect vector.
Authors: Hoh, F. / Uzest, M. / Drucker, M. / Plisson-Chastang, C. / Bron, P. / Blanc, S. / Dumas, C.

History

Deposition	Nov 6, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Nov 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3f6n.cif.gz	67.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3f6n.ent.gz	49.5 KB	Display	PDB format
PDBx/mmJSON format	3f6n.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3f6n_validation.pdf.gz	449.8 KB	Display	wwPDB validaton report
Full document	3f6n_full_validation.pdf.gz	452.3 KB	Display
Data in XML	3f6n_validation.xml.gz	11.1 KB	Display
Data in CIF	3f6n_validation.cif.gz	14.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f6/3f6n ftp://data.pdbj.org/pub/pdb/validation_reports/f6/3f6n	HTTPS FTP

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Related structure data

Related structure data	3k4tC 1t6fS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2ztb-1 6wjk-d 6ual-d 2ztb-2 1sfc-3 5afo-2 3k4t-d 1sfc-2 3zjx-4 5fn6-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Virion-associated protein

B: Virion-associated protein

C: Virion-associated protein

D: Virion-associated protein

56.7 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	104.943, 104.943, 72.527
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	172
Space group name H-M	P6₄

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASN	ASN	SER	SER	4	A	A	3 - 34	3 - 34
2	1	ASN	ASN	SER	SER	4	B	B	3 - 34	3 - 34
3	1	ASN	ASN	SER	SER	4	C	C	3 - 34	3 - 34
4	1	ASN	ASN	SER	SER	4	D	D	3 - 34	3 - 34
1	2	GLN	GLN	LYS	LYS	4	A	A	35 - 48	35 - 48
2	2	GLN	GLN	LYS	LYS	4	B	B	35 - 48	35 - 48
3	2	GLN	GLN	LYS	LYS	4	C	C	35 - 48	35 - 48
4	2	GLN	GLN	LYS	LYS	4	D	D	35 - 48	35 - 48
1	3	ILE	ILE	ASN	ASN	4	A	A	49 - 63	49 - 63
2	3	ILE	ILE	ASN	ASN	4	B	B	49 - 63	49 - 63
3	3	ILE	ILE	ASN	ASN	4	C	C	49 - 63	49 - 63
4	3	ILE	ILE	ASN	ASN	4	D	D	49 - 63	49 - 63
1	4	LYS	LYS	ALA	ALA	5	A	A	64 - 69	64 - 69
2	4	LYS	LYS	ALA	ALA	5	B	B	64 - 69	64 - 69
3	4	LYS	LYS	ALA	ALA	5	C	C	64 - 69	64 - 69
4	4	LYS	LYS	ALA	ALA	5	D	D	64 - 69	64 - 69

NCS ensembles :

ID
1
2
3
4

#1: Protein	Virion-associated protein / virion associated protein P3 / Vap / DNA-binding protein Mass: 14168.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cauliflower mosaic virus (STRAIN STRASBOURG) Strain: Strasbourg / Gene: ORF III, ORF-3 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P03551
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.54 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% PEG 1000, 0.1M MES-NaOH buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.931 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. all: 8377 / Num. obs: 8369 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / B_iso Wilson estimate: 90.5 Å² / R_merge(I) obs: 0.065 / R_sym value: 0.065 / Net I/σ(I): 16.5
Reflection shell	Resolution: 3.1→3.27 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.306 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1228 / R_sym value: 0.46 / % possible all: 99.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing
REFMAC	5.5.0053	refinement
PDB_EXTRACT	3.006	data extraction
ADSC	Quantum	data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T6F

1t6f

Resolution: 3.1→20.85 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.889 / Occupancy max: 1 / Occupancy min: 1 / SU B: 47.511 / SU ML: 0.373 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.287	918	11 %	RANDOM
R_work	0.222	-	-	-
all	0.231	8338	-	-
obs	0.229	8336	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso max: 47.64 Å² / B_iso mean: 36.293 Å² / B_iso min: 16.93 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.15 Å²	-0.07 Å²	0 Å²
2-	-	-0.15 Å²	0 Å²
3-	-	-	0.22 Å²

Refine analyze

Luzzati coordinate error obs: 0.765 Å

Refinement step

Cycle: LAST / Resolution: 3.1→20.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2203	0	0	1	2204

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	2214
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.037	2.016	2985
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.797	5	285
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.421	30	87
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.87	15	474
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	377
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	1532
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.199	1.5	1444
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.437	2	2343
X-RAY DIFFRACTION	r_scbond_it	0.883	3	770
X-RAY DIFFRACTION	r_scangle_it	1.655	4.5	642
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	247	MEDIUM POSITIONAL	0.35	0.5
1	2	B	247	MEDIUM POSITIONAL	0.39	0.5
1	3	C	247	MEDIUM POSITIONAL	0.47	0.5
1	4	D	247	MEDIUM POSITIONAL	0.52	0.5
1	1	A	247	MEDIUM THERMAL	0.29	2
1	2	B	247	MEDIUM THERMAL	0.3	2
1	3	C	247	MEDIUM THERMAL	0.32	2
1	4	D	247	MEDIUM THERMAL	0.27	2
2	1	A	106	MEDIUM POSITIONAL	0.56	0.5
2	2	B	106	MEDIUM POSITIONAL	0.54	0.5
2	3	C	106	MEDIUM POSITIONAL	0.52	0.5
2	4	D	106	MEDIUM POSITIONAL	0.64	0.5
2	1	A	106	MEDIUM THERMAL	0.33	2
2	2	B	106	MEDIUM THERMAL	0.19	2
2	3	C	106	MEDIUM THERMAL	0.16	2
2	4	D	106	MEDIUM THERMAL	0.2	2
3	1	A	114	MEDIUM POSITIONAL	0.3	0.5
3	2	B	114	MEDIUM POSITIONAL	0.28	0.5
3	3	C	114	MEDIUM POSITIONAL	0.32	0.5
3	4	D	114	MEDIUM POSITIONAL	0.29	0.5
3	1	A	114	MEDIUM THERMAL	0.19	2
3	2	B	114	MEDIUM THERMAL	0.19	2
3	3	C	114	MEDIUM THERMAL	0.15	2
3	4	D	114	MEDIUM THERMAL	0.17	2
4	1	A	24	MEDIUM POSITIONAL	0.12	0.5
4	2	B	24	MEDIUM POSITIONAL	0.18	0.5
4	3	C	24	MEDIUM POSITIONAL	0.09	0.5
4	4	D	24	MEDIUM POSITIONAL	0.17	0.5
4	1	A	24	LOOSE POSITIONAL	0.68	5
4	2	B	24	LOOSE POSITIONAL	0.76	5
4	3	C	24	LOOSE POSITIONAL	0.64	5
4	4	D	24	LOOSE POSITIONAL	0.43	5
4	1	A	24	MEDIUM THERMAL	0.28	2
4	2	B	24	MEDIUM THERMAL	0.19	2
4	3	C	24	MEDIUM THERMAL	0.36	2
4	4	D	24	MEDIUM THERMAL	0.57	2
4	1	A	24	LOOSE THERMAL	0.26
4	2	B	24	LOOSE THERMAL	0.23
4	3	C	24	LOOSE THERMAL	0.26
4	4	D	24	LOOSE THERMAL	0.38

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.386	72	-
R_work	0.287	543	-
all	-	615	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	17.1652	-0.1849	-3.2191	0.2571	-0.1928	1.193	-0.1571	0.3152	0.153	0.0098	0.1938	0.057	-0.0722	0.0698	-0.0366	0.319	0.0584	-0.006	0.4478	0.0818	0.0194	-5.002	13.891	25.151
2	14.4659	3.264	-0.4179	0.7507	-0.0234	0.4463	0.0146	-1.4639	0.4091	-0.0239	-0.1969	0.1093	-0.3172	0.5876	0.1824	0.6683	-0.1236	-0.1176	1.0672	0.0716	0.289	24.11	13.974	24.166
3	14.6544	0.5166	1.585	1.19	-0.6851	3.1295	0.2567	-0.198	0.3492	0.1501	-0.0903	0.1837	0.0298	-0.4493	-0.1664	0.3962	-0.0577	-0.029	0.6656	0.0365	0.1467	43.466	13.643	23.707
4	16.9822	2.5234	2.4667	6.6384	0.8797	0.7227	0.3184	1.118	-0.6874	-0.1037	-0.223	0.1406	0.2742	0.0716	-0.0954	0.4252	0.0336	-0.0264	0.6179	0.0923	0.1631	69.262	12.454	22.433

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 31
2	X-RAY DIFFRACTION	1	B	2 - 31
3	X-RAY DIFFRACTION	1	C	2 - 31
4	X-RAY DIFFRACTION	1	D	3 - 31
5	X-RAY DIFFRACTION	2	A	32 - 39
6	X-RAY DIFFRACTION	2	B	32 - 39
7	X-RAY DIFFRACTION	2	C	32 - 39
8	X-RAY DIFFRACTION	2	D	32 - 39
9	X-RAY DIFFRACTION	3	A	40 - 57
10	X-RAY DIFFRACTION	3	B	40 - 57
11	X-RAY DIFFRACTION	3	C	40 - 57
12	X-RAY DIFFRACTION	3	D	40 - 57
13	X-RAY DIFFRACTION	4	A	58 - 72
14	X-RAY DIFFRACTION	4	B	58 - 75
15	X-RAY DIFFRACTION	4	C	58 - 74
16	X-RAY DIFFRACTION	4	D	58 - 74

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